Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.20.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.60109	0.428
27DAP/17DAP	1.37757	0.761
39DAP/27DAP	0.75854	0.421
41DAP/39DAP	1.415	0.422
42DAP/41DAP	0.98316	1
43DAP/42DAP	1.10236	0.94
47DAP/43DAP	1.28242	0.943
52DAP/47DAP	1.07219	0.908
57DAP/52DAP	1.17956	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00568	1
17DAP/reference	1.19619	0.148
27DAP/reference	1.38579	0.227
39DAP/reference	1.01459	0.816
41DAP/reference	1.09889	0.91
42DAP/reference	0.94936	0.295
43DAP/reference	0.68599
47DAP/reference	0.99568	0.72
52DAP/reference	0.90488	0.183
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82056	0.363
27DAP/17DAP	1.02232	0.919
39DAP/27DAP	1.39196	0.343
41DAP/39DAP	0.84501	0.333
42DAP/41DAP	1.26002	0.343
43DAP/42DAP	1.17026	0.513
47DAP/43DAP	0.96099	0.833
52DAP/47DAP	1.19982	0.478
57DAP/52DAP	1.10329	0.818
57DAP/7DAP	0.81468	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90658	0.27
17DAP/reference	0.94707	0.22
27DAP/reference	0.84751	0.051
39DAP/reference	0.67479	0.018
41DAP/reference	0.67828	0.018
42DAP/reference	0.65093	0.01
43DAP/reference	0.89142	0.183
47DAP/reference	1.10672	0.996
52DAP/reference	0.99088	0.679
57DAP/reference	0.76879	0.064

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98373	0.756
17DAP/reference	0.96956	0.51
27DAP/reference	0.76396	0.056
39DAP/reference	0.89974	0.173
41DAP/reference	0.86408	0.105
42DAP/reference	0.7741	0.019
43DAP/reference	0.94547	0.43
47DAP/reference	0.93518	0.071
52DAP/reference	0.94254	0.239
57DAP/reference	0.96669	0.519

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75556	0.214
17DAP/reference	0.90072	0.348
27DAP/reference	0.8495	0.045
39DAP/reference	0.85557	0.016
41DAP/reference	0.76759	0.022
42DAP/reference	0.78661	0.016
43DAP/reference	0.81382	0.102
47DAP/reference	0.80411	0.057
52DAP/reference	1.16436	0.779
57DAP/reference	0.60382	0.027

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02259	1
26DAP/20DAP	1.86984	0.102
34DAP/26DAP	0.81082	0.741
51DAP/34DAP	1.03181	0.96
52DAP/51DAP	0.89336	1
53DAP/52DAP	1.25031	0.806
55DAP/53DAP	1.12564	0.671
57DAP/55DAP	1.34743	0.666
62DAP/57DAP	1.17696	0.833
68DAP/62DAP	0.89962	0.7
68DAP/14DAP	1.1914	0.578

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.57165	0.043

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70507	0.207
Mature Green Tomato/Ripe Tomato	0.71825	0.107
Immature Eggplant/Mature Eggplant	1.498	0.105
Ripe Pepper/Ripe Tomato	0.7305	1
Mature Eggplant/Ripe Tomato	0.74418	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04128	0.877
1-1-2/M82	1.0332	1
12-2/M82	1.18402	1
12-4/M82	0.99053	1
1-3/M82	0.96021
2-1-1/M82	1.01506	1
2-1/M82	1.20005
2-6/M82	0.86069	1
3-2/M82	0.92796	1
4-1-1/M82	0.88219	1
4-1/M82	1.05949	1
4-3-2/M82	0.80648	0.487
4-3/M82	1.04569	1
5-3/M82	0.97608	1
6-2/M82	1.11008
6-3/M82	1.00049	1
7-1/M82	0.83121	0.509
7-2/M82	0.86514
9-3-2/M82	0.95394

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.81036
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.64014	0.52
IL1-4/WTpooled	1.69536	1
WT/WTpooled	1.38624

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.10202	0.309

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.85003	1
DC3000/delta hrp 6h	0.77198	0.891
DC3000/delta hrp 12h	1.17128	1
DC3000/delta hrp 24h	0.93966	0.692

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.23363
DC3000 delta B/DC3000 delta AB	1.11881	0.516

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92345	1
Exp 36h	1.11225	1
Exp 60h	1.02031	1

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	0.96552	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.05315	0.736
Var 12h NI row2-row1	0.82659	0.546
Var 36h I row2-row1	0.85909	0.438
Var 36h NI row2-row1	1.41945	0.482
Var 60h I row2-row1	0.76364	0.285
Var 60h NI row2-row1	0.96757	1
Time course 0hI-0hNI	1.02055	1
Time course 12hI-12hNI	1.08774	0.544
Time course 36hI-36hNI	1.02558	0.975
Time course 60hI-60hNI	1.24841	0.06

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.0429	0.612
transgenic ySAMdc/azygous control (breaker)	0.93063	0.49
transgenic ySAMdc/azygous control (red)	1.11838	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95087	0.146

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02903	1

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99974	1
Manapal/WT (break)	0.82676	0.333
Manapal/WT (red)	0.70929	0.181